%0 Journal Article
%T CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies
%A Robert Lawrence
%A Aaron G Day-Williams
%A Katherine S Elliott
%A Andrew P Morris
%A Eleftheria Zeggini
%J BMC Bioinformatics
%D 2010
%I BioMed Central
%R 10.1186/1471-2105-11-527
%X We have developed two software tools, CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait), which enable efficient large-scale analysis of low frequency and rare variants. Both programs implement a collapsing method examining the accumulation of low frequency and rare variants across a locus of interest that has more power than single variant analysis. CCRaVAT carries out case-control analyses whereas QuTie has been developed for continuous trait analysis.CCRaVAT and QuTie are easy to use software tools that allow users to perform genome-wide association analysis on low frequency and rare variants for both binary and quantitative traits. The software is freely available and provides the genetics community with a resource to perform association analysis on rarer genetic variants.Recent advances in high-throughput genotyping have made large-scale genetic association studies possible. Genome-wide association studies (GWAS) for complex disease have met with unprecedented success in identifying common susceptibility variants. However, the discovered common-frequency single nucleotide polymorphism (SNP) associations do not account for a large proportion of the genetic component of disease. The field is now focusing on the analysis of low frequency and rare variants (i.e. minor allele frequency (MAF) ¡Ü0.05) to investigate if they will help explain the missing heritability in complex trait etiology [1,2]. While the sample sizes currently investigated are large enough for a well-powered GWAS of common variants, they are not large enough to provide sufficient power for the single-point analysis of low frequency/rare variants with small to moderate effect sizes [3]. We have developed association analysis software, CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait), which allow the large-scale analysis of low frequency/rare polymorphisms. The software increases power over single marker analysis of these variants by pooli
%U http://www.biomedcentral.com/1471-2105/11/527